rs1558902
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001080432.3(FTO):c.46-40478T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,962 control chromosomes in the GnomAD database, including 8,797 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 8797 hom., cov: 31)
Consequence
FTO
NM_001080432.3 intron
NM_001080432.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.355
Genes affected
FTO (HGNC:24678): (FTO alpha-ketoglutarate dependent dioxygenase) This gene is a nuclear protein of the AlkB related non-haem iron and 2-oxoglutarate-dependent oxygenase superfamily but the exact physiological function of this gene is not known. Other non-heme iron enzymes function to reverse alkylated DNA and RNA damage by oxidative demethylation. Studies in mice and humans indicate a role in nervous and cardiovascular systems and a strong association with body mass index, obesity risk, and type 2 diabetes. [provided by RefSeq, Jul 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.309 AC: 46860AN: 151844Hom.: 8801 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
46860
AN:
151844
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.308 AC: 46845AN: 151962Hom.: 8797 Cov.: 31 AF XY: 0.309 AC XY: 22974AN XY: 74258 show subpopulations
GnomAD4 genome
AF:
AC:
46845
AN:
151962
Hom.:
Cov.:
31
AF XY:
AC XY:
22974
AN XY:
74258
Gnomad4 AFR
AF:
AC:
0.101678
AN:
0.101678
Gnomad4 AMR
AF:
AC:
0.288822
AN:
0.288822
Gnomad4 ASJ
AF:
AC:
0.510957
AN:
0.510957
Gnomad4 EAS
AF:
AC:
0.153891
AN:
0.153891
Gnomad4 SAS
AF:
AC:
0.331255
AN:
0.331255
Gnomad4 FIN
AF:
AC:
0.423631
AN:
0.423631
Gnomad4 NFE
AF:
AC:
0.417018
AN:
0.417018
Gnomad4 OTH
AF:
AC:
0.338082
AN:
0.338082
Heterozygous variant carriers
0
1494
2988
4483
5977
7471
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
468
936
1404
1872
2340
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
941
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at